Fungus Fuels Tree GrowthPoplar is the fastest growing hardwood tree in the western United States, making it an energy feedstock of particular interest to the U.S. Department of Energy (DOE). The fungus is almost always found among and within poplar trees, and in an effort to understand its influence on the plant, a team of scientists studied what happens to the tree’s physical traits and gene expression when the fungus is present.

Better Genome Editing for BioenergyCRISPR-Cas9 is a powerful, high-throughput gene-editing tool that can help scientists engineer organisms for bioenergy applications. Cas9 needs guide RNA to lead it to the correct sequence to snip—but not all guides are effective. Researchers created a set of guide RNAs that were effective against 94 percent of the genes in a lipid-prolific yeast.

Cultivating Symbiotic Antarctic MicrobesIn the Proceedings of the National Academy of Sciences, researchers employed multiple microbiology and ‘omics techniques to experimentally determine that Nanohaloarchaeota are not free-living archaea but rather symbionts.

Methane Flux in the AmazonWetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.

Insights into Functional Diversity in NeurosporaThis proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.

Improving the Cacao Genome and PhytozomeAn updated reference genome for Theobroma cacao Matina 1-6 has now been completed and released by HudsonAlpha scientists, with the help of Mars Wrigley funding. The annotated genome has been updated to a high quality modern standard and includes RNA-seq data. The improved genome is available for comparative purposes on the latest version of the JGI plant portal Phytozome (phytozome-next.JGI.doe.gov).

Mining IMG/M for CRISPR-Associated ProteinsResearchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at UC Berkeley.

What Happens Underground Influences Global Nutrient CyclesThrough the Facilities Integrating Collaborations for User Science (FICUS) program, the Environmental Molecular Sciences Laboratory (EMSL) and the DOE Joint Genome Institute (JGI) have selected 11 proposals for support from 53 received through a joint research call.

CSP Functional Genomics Call OngoingThe CSP Functional Genomics call is to enable users to perform state-of-the-art functional genomics research and to help them translate genomic information into biological function. Proposals submitted by January 31, 2019 will be part of the next review.

Learning to LookUsing machine learning, JGI researchers combed through more than 70,000 microbial and metagenome datasets, ultimately identifying more than 10,000 inovirus-like sequences compared to the 56 previously known inovirus genomes.

JGI Early Career Researchers in mSystems Special IssueJGI researchers are among the authors who offer perspectives on what the next five years of innovation could look like. In one article, Rex Malmstrom and Emiley Eloe-Fadrosh outline more targeted approaches to reconstruct individual microbes in an environmental sample. In a separate article, Simon Roux makes a pitch for readers to get involved in the developing field of virus ecogenomics.

Hidden Giants in Forest SoilsIn Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. Most of the genomes were uncovered using a "mini-metagenomics" approach that reduced the complexity of the soil microbial communities sequenced and analyzed.

Susannah Tringe – Microbial Systems

Research in the Tringe group focuses on sequence-based approaches to studying microbial community assembly, function and dynamics. Members of the group aid in communicating and interpreting sequencing results to collaborators in addition to performing collaborative and independent research in microbial community genomics. Major foci of these research efforts are the roles of microbial communities in wetland carbon cycling and the interactions of plants with their associated microbiomes.

Microbiology of produced water recycling

Hydrocarbon extraction through methods such as hydraulic fracturing produces large volumes of chemically contaminated produced water that must be managed and disposed of appropriately. There is interest in exploiting produced water for crop irrigation, especially in drought-prone areas, but treatment is necessary to remove the diverse chemical components, many of which are potentially toxic to plants, animals and humans. Biological treatment methods are effective at removing many contaminants found in produced water, but the microbial communities inhabiting the treatment reactors have been minimally characterized and thus exhibit variable performance that is challenging to optimize.

We aim to characterize the microbial communities found in bioreactors treating produced water and assign key activities to specific organisms, using metagenome sequencing, genome binning and metabolic reconstruction. Additionally, we would also cultivate and study individual members of these communities based on their predicted metabolisms, in order to construct stable defined consortia for produced water treatment.

Wetland greenhouse gas cycling

Wetlands occupy less than 10% of the Earth’s land surface but harbor up to a third of soil organic carbon. Wetland preservation and restoration has the potential to sequester significant amounts of terrestrial carbon, but they can also produce the potent greenhouse gas methane, meaning different types of wetlands may serve as either greenhouse gas sources or sinks. This uncertainty leads to considerable variability in predictions from climate models, both in the overall carbon budget and in how wetlands are expected to respond to climate change.

More accurate prediction of wetland carbon dynamics requires better understanding of the belowground microbial communities that are key to recycling or storing biomass carbon and producing greenhouse gases. To gain insight into these systems we are applying microbial community genomics to wetland microbial communities in coastal wetlands across the San Francisco Bay / Delta region, including in-depth metagenome and metatranscriptome sequencing of natural and restored wetlands. (Watch the video here.) These studies are revealing organisms and genes involved in promoting or repressing greenhouse gas emissions, enabling a mechanistic understanding of belowground carbon cycling. Ultimately these findings are expected to aid in planning wetland restoration projects to maximize carbon storage. Download a copy of the JGI wetlands handout.

Plant-microbe interactions

The interactions of plants with microbial communities found in the endosphere and rhizosphere (within plant tissues and adjacent to the roots) have been shown to be critical to plant growth, health and disease resistance and manipulation of these organisms could potentially improve yields of both bioenergy and food crops. Yet how these communities form and to what extent plants exert active control over the organisms involved is largely unknown, and genomic investigation of endophytic and rhizosphere microbes has been largely confined to culture-based methods due to both the challenges associated with soil metagenomics described above, and the close association with plant cells which harbor large and complex genomes. In close collaboration with Jeff Dangl at the University of North Carolina, we are addressing these obstacles with high-throughput 16S profiling of rhizosphere and endophyte communities combined with single cell genomics, metagenomics and metatranscriptomics to characterize key plant-associated microbes, using Arabidopsis thaliana as a plant model system. These investigations have revealed reproducible rhizosphere and endophyte community assemblage and plant genotype-specific associations with rhizosphere organisms. Ultimately, this work will allow us to identify genes, proteins and molecules involved in plant-microbe and microbe-microbe interactions in the plant root environment.

Group Members

Jinglie received his Ph.D. degree in biological science from Auburn University. His research interests include metagenomic analysis, viral genome analysis, carbon cycling in wetlands and arbuscular mycorrhizal fungi associating with sorghum roots. He also has a background in bioinformatics, machine learning, data engineering and statistics.

Shwetha holds a Ph.D. in Urban Engineering from The University of Tokyo and specializes in water and wastewater microbiology. She is investigating microbial communities involved in biological treatment of produced water.

Kyle completed his Ph.D. at the University of Zürich and Agroscope, a Swiss federal research institute. His current research uses DNA sequence-based methods to investigate how nutrient and water stress influence host-microbe and microbe-microbe interactions in sorghum-associated microbial communities.

Mo Kaze, Affiliate

Xiaohui Li, Affiliate

Mo Kaze is finishing up her PhD at the University of California, Merced in Quantitative Systems Biology. Her DOE SCGSR Fellowship project at JGI examines carbon flux and microbial community structure in engineered interfaces between aquatic and terrestrial systems.

Xiaohui is a visiting scholar from Ningbo University, China. He is interested in mechanisms of interaction between plants and microorganisms. At JGI, he is investigating the rhizosphere microbiome of sorghum in order to clarify their roles in plant abiotic stress.

Group Alumni

Dawn Chiniquy is a Project Scientist in the Deutschbauer lab at Lawrence Berkeley National Laboratory